Several approaches have been described for differential staining of blastocysts, but these methods are often time-consuming and unreliable. Here we describe a method for simultaneous differential staining and detection of apoptosis. The differential staining is based on the transcription factor CDX2 which is localized in the nucleus of trophectoderm (TE) cells but absent in the inner cell mass (ICM). Apoptosis is detected by staining of active caspase-3, a key player in several apoptotic pathways. This new approach represents a robust method for quantifying simultaneously ICM/TE ratio and apoptotic cell ratio in bovine, murine, porcine, and human blastocysts.